[Bioclusters] Re: pe's with SGE 6.0

[Chris Dagdigian]

Hi Glen,

Parallel environments (PE's) are "mostly" the same in Grid Engine 6 vs 
5.3 in my experience.

The main "gotcha" difference is that in SGE 6 you tell the *qeueue* the 
list of PE's it is able to support while in SGE 5 the opposite occured 
-- the PE itself was configured with a list of queues that it was active 
in. The other addition is the "urgency_slots" param (I think) which was 
not in SGE 5.3.

If you had PE definitions or deployment scripts that worked in SGE 5.3 
but not in 6 it may be due to the above. The "pe_list" parameter has 
moved from the PE object itself and into the queue configuration.

For SGE 6 there are still the usual PVM and MPI templates and examples 
that come with the distribution.  Just look in $SGE_ROOT/pvm/ and 
$SGE_ROOT/mpi/.

Reuti also just updated the Grid Engine tight LAMMPI HOWTO which is here:

http://gridengine.sunsource.net/project/gridengine/howto/lam-integration/lam-integration.html

Back to PE's ...

This is what a generic loosely integrated MPICH PE would look like in SGE 6:

> workgroupcluster:~ admin$ qconf -sp  mpich
> pe_name           mpich
> slots             512
> user_lists        NONE
> xuser_lists       NONE
> start_proc_args   /common/sge/mpi/startmpi.sh $pe_hostfile
> stop_proc_args    /common/sge/mpi/stopmpi.sh
> allocation_rule   $fill_up
> control_slaves    FALSE
> job_is_first_task TRUE
> urgency_slots     min

Note that there is no list of queues that the PE runs in. This has moved.

The "pe_list" is now part of the queue configuration:

> workgroupcluster:~ admin$ qconf -sq all.q
> qname                 all.q
> hostlist              @allhosts
> seq_no                0
> load_thresholds       np_load_avg=1.75
> suspend_thresholds    NONE
> nsuspend              1
> suspend_interval      00:05:00
> priority              0
> min_cpu_interval      00:05:00
> processors            UNDEFINED
> qtype                 BATCH INTERACTIVE
> ckpt_list             NONE
> pe_list               make mpich
> rerun                 FALSE
< .... SNIP .... >


I've tried to list the differences between Grid Engine 5 and Grid Engine 
6 at this URL:

http://bioteam.net/dag/gridengine-6-features.html

Not sure if I got it all but feedback/corrections are welcome.




Regards,
Chris






Glen Otero wrote:

> I think I broke something while playing with grid engine 6.0, 
> pvm-3.4.4-19, and mpich2. Anyone have pvm and mpi/mpich templates that 
> they know work in creating pe's with SGE 6.0?
> 
> Thanks!
> 
> Glen
> 
> Glen Otero Ph.D.
> 

-- 
Chris Dagdigian, <dag at sonsorol.org>
BioTeam  - Independent life science IT & informatics consulting
Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E iChat/AIM: bioteamdag  Web: http://bioteam.net